Is There A Web Based Tool For Fixing Pdb Protein Structures That May Have Missing Atoms?

Question

[Flow]

Some protein files from PDB database have missing atoms, so when I use them with some molecular modeling programs, they complain about it. Is it there any web server that can fix/heal them? SOmebody told me about MODELLER, but as far as I know they do not have a server.

[aravind ramesh]

http://www.ebi.ac.uk/pdbsum/ might be useful for you.

[Flow]

thanks, but that is just a database, I do not see how that could fix the protein !

Answer 1

[João Rodrigues]

Hi,

Use this interface for MODELLER, you should be able to upload your template (your incomplete protein structure) and paste the sequence alignment between your sequence and your protein (essentially, the same sequence repeated twice).

The only thing you need is the MODELLER key, which you can get in the MODELLER website upon registration for a license (for free).

Answer 2

[quentin.delettre]

Construct missing side chains from PDB file

Another biostar thread about missing things

Or as previously mentionned, Modeller.

[Flow]

thanks but second link does not worl

[quentin.delettre]

Strange. Here it is : Adding missing atoms to PDB